InterMine Mobile

Tag: gsoc

TL;DR: Send us your awesome project ideas and/or volunteer to be a mentor!

Longer version:

We need your ideas!

GSoC 2019 has been announced, and as in 2017 and 2018, InterMine will be applying again to become a mentor organisation. This means we’re back at the “we want your project ideas!” phase – and we do! If you work with or use an InterMine and have ideas for its improvement – might it be something big enough for a student to work on for three months? Any of these types of ideas would be great:

An interesting exploratory project that answers a question – “is x likely to be possible or practical with InterMine?”

Fixing something that’s always bothered you – in 2018, we managed this with the Solr Search update!

Could you mentor for an InterMine project?

In 2017 and 2018 we’ve had mentors from the community, including mentors who were previously GSoC students. Ideally, interested mentors should be known to us, perhaps because you are an InterMine user, developer/maintainer/administrator, or a previous student. If you don’t have any project ideas of your own, you may be able to pick one from the project list that suits your skills and interests.

What is mentoring like, you might ask? We have the basics set out in our mentor terms and conditions (which isn’t as dry as the title suggests). Some things to note:

The busiest period is the application phase, when multiple students will be interacting with you to learn about and contribute to the community.

After this, things calm down a lot. You’re expected to meet (virtually) with your student at least once a week for the three months of the coding phase. Proactive students often only need an hour or two here or there, but other students may need more hands-on attention.

Students wages are paid by Google. Mentors also get a small stipend and thank-you gift after GSoC is complete.

You’ll be paired with a Cambridge-based mentor for support, guidance, and cover while on vacation.

A great opportunity all around

GSoC as a program ends up being incredibly valuable two-way exchange. Students get three months of paid work experience at an open source organisation, and on the other side InterMine and InterMine mentors end up with the chance to guide projects and see some truly fantastic work implemented. Promising students might even end up applying for vacancies when they come up – it’s a great way to broaden your community!

InterMine 3.0 is now available and features a brand new search powered by Solr.

Default search configuration will work well, but Solr allows for endless configuration for your specific needs.

Now the first search after deployment is instant, you can inspect the search index directly (via http://localhost:8983/solr/) and there’s a facet web service (via /service/facet-list and /service/facets?q=gene). Certain bugs, e.g. searching for the gene “OR”, are also now fixed.

New Configuration Option – optimize

There is a new keyword search configuration setting: index.optimize. If set to `true`, reorganises the index so chunks are placed together in storage which might improve the search time. (Similar to defragmentation of a hard disk.) See the configuration docs for more details.

One of the goals of Google Summer of Code (GSoC) is to help turn students into long-term open source maintainers and contributors. I suspect we’ve managed this with our current batch of students, who have contributed to our projects across a broad range of topics, whether it was querying InterMine using natural language sentences, updating our search capabilities (both UIs and search backends), or adding new features to the InterMine python client.

From the start of the application process, our fabulous pool of applicants spent time interacting with each other and even helping each other out before anyone had been officially accepted. We received numerous PRs, tickets, and suggestions on our GitHub repos, and for this year we had returning GSoC mentors who previously had been students. It’s almost hard to believe we hadn’t participated before 2017, seeing all of the great work and enthusiasm GSoC brings, all while being able to pay students for their time and give them valuable work experience.

To wrap up this year’s great set of projects we had a community call [agenda & notes here] where our students presented their work in roughly 5 minute slots. You can catch up on each of the recorded presentations in our GSoC 2018 playlist, or here are direct links to each of the videos:

Currently InterMine uses Apache Lucene (v3.0.2) library to index the data and provide a key-word style search over all data. The goal of this project is to introduce Apache Solr in InterMine so that indexing and searching can happen even quicker. Unlike Lucene which is a library, Apache Solr is a separate server application which is similar to a database server. We setup and configure Solr (v.7.2.1) independently from the application. We use Solr clients to communicate between the application and the Solr instance.

Here, SolrJ (v.7.2.1), a java client for solr is used to communicate between the InterMine and Solr. We also removed the bobo facet library which is used with Lucene since Solr itself provides faceted search. The implementations has been designed in a manner that InterMine would not be heavily coupled with Solr. When you want to change your search engine to something else in future, you just have make different implementations for the interfaces defined.

Currently the search index and the autocomplete index processes use Solr to index the data. The index time has improved significantly with compared to previous indexing times. For example, currently FlyMine takes around around 1900 seconds (32 mins) to index the data. But with Solr we see that it takes only 1250 seconds (21 mins) which is 34% reduction in time. Query time has also improved with Solr where a query of “*:*” in FlyMine would take around 30-40 seconds which with Solr takes less than 1 second. Previously with Lucene, the indexed data has to be retrieved from the database during the first search after starting the webapp. This took some time but with Solr, it is not the case and the results are instantly returned.

Addition to the above, two web services have been implemented. A Facet service has been implemented which will return only the facet counts for a particular query rather than returning all the results. The other web service is Facet List service which is similar to the previous one but it will return all the facets available in a mine. It will be useful when you want to know all the facets in a mine before you run an actual search.

All these changes are made against InterMine 2.0 version. These changes will be included in an InterMine release in near future, but for those who want to try these changes immediately, can checkout this branch in Github and follow these instructions. All these changes are tested with Apache Solr (v7.2.1).

The GSoC 2018 is coming to its end, and after 3 months of hard work, I can proudly present a summary of all our achievements during this summer of code.

Summary of Project Goals

InterMine is a open source Data Warehouse intended to be used for the integration and analysis of complex biological data. With InterMine, you can explore organism and other research data provided by different organizations, moving between databases using criteria such as homology.

The existing query builder in InterMine requires some experience to obtain the desired data in a mine, which can become overwhelming for new users. For instance, for a user interested on searching data in HumanMine using its query builder, he or she would need to browse through the different classes and attributes, choosing between the available fields and adding the different constraints over each of them, in order to get the desired output.

For example, a simple query you might want to glean from InterMine might be as follows:

Problem: This query sounds simple-ish, but building it in our query builder requires a strong familiarity with the data model, and can be confusing for anyone new to InterMine. We would like the data browser to be more complex than the simplicity of a simple keyword search, but less complex than the current query builder. For context, here’s the humanmine query builder: http://www.humanmine.org/humanmine/customQuery.do. We have attached a screenshot of what it looks like for the homology query mentioned above, where it can be seen why it looks a little intimidating.

This requires the user to have a decent knowledge of the model schema in order to successfully build a correct query for the expected query results. For new users this workflow can become, indeed, overwhelming to search for specific information in the data.

For this reason the goal of this project is to implement a faceted search tool to display the data from InterMine database, allowing the users to search easily within the different mines available around InterMine, without the requirement of having an extensive knowledge of the data model.

Summary of Project Achievements

In order to maintain a good workflow, the project was divided into three major versions or milestones, coinciding the deadline of each one with GSoC evaluation phases. The main developments in each milestone are listed below, and comprises a total of 67 closed issues with 194 commits.

Milestone 1 (June 11). In the first milestone (related GitHub issue here), the following features were added:

In the following figure, the different elements available on the browser interface are displayed and further explained.

As depicted above, the user is able to change between the different mines available in the InterMine registry by using the dropdown box in (1). Next, in (2) the viewed class can be changed, and currently it can be either Genes or Proteins. Moreover, in (3), the different filters available in the currently explored mine are displayed, where the user can filter the data shown in the table at (6) that better fulfills his/her requirements. Furthermore, some plots regarding to the data in the table are displayed on (4). Currently it shows a pie chart of individuals per different organism, but it will be extended with more plots in the future. Finally, the user has the option to save the table as list, generate the code to embed it elsewhere, or to export the results by using the options in (5).

There are already some features to be added to the browser after GSoC, some of them are, for instance, to allow users to add their personal InterMine’s API tokens for each mine and use them for the Save as List functionality of the table (link). Another useful feature that I wasn’t able to implement due to a temporary disabling in the InterMine ontology was a Phenotypes filter (link). Next, a new histogram plot to the top section about Gene length will be added (link). Furthermore, a “current class” filter will be added to the sidebar (link). Finally, another desirable feature would be to refactor the per-mine filters to use path query (link).

As a conclusion, the fact that the final product has been tested and is going to be truly helpful for the target community of users, is enough for me to be proud of the developed tool during this Google Summer of Code. Also the results of this project will allow us to, hopefully, publish a paper describing the new InterMine browser.

It has been three weeks since the commencement of the GSoC’18 Coding Phase and a lot of progress has been made till now. The project has been deployed here.

This week has been really very productive. I have worked upon several parts of the application this week. My main focus for this week was to add filters into the application. But I ended up with some more cool stuff here 😉
Let’s have a look at all of them one by one.

Search Rating/Relevance Score

The application knows what you are searching for 😉

Relevance score is a value which is calculated by the InterMine QuickSearch API endpoint for every keyword which is searched. This rating determines how much relevant is the result item with the search keyword. The QuickSearch API response provides a floating value of ‘relevance’ parameter. InterMine uses a formula for determining the Search score in the specific InterMine Search Portals. I have used the same formula to convert the floating relevance score into a score out of 5. The formula is here:
=> Math.round(Math.max(0.1, Math.min(1, relevance)) * 5)

2. Different colors for different Categories in Results

The world is colorful and hence our app too 😉

This was a feedback received from the InterMine community. Having different category results shaded in different colors helps in exploring the results easily. At times, there may be a long list of result items returned by the application. Then having separate colors for separate categories helps us to explore faster. Our eyes are meant to perceive colors more quickly than text.

3. External links to reports

Every result item has a link which opens the result report on its particular InterMine portal. This report page contains more detailed information about the result item. On clicking the icon, a new tab with the given result report opens in the browser. The result link is generated dynamically:

4. Metadata about search results

Metadata for BMAP mine (search: ‘brca1′)

Having metadata about the results returned is always handy at work. Every tab in the application loads a set of metadata as attached above. This can certainly help in understanding the presence of a search term in the mine in a unified way.

5. Search/Relevance Score Filter

Score filter on sidebar of the application

With addition of score/relevance in the application, it was very much necessary to add an option to filter the results based on that. This section provides radio buttons to filter out the results based on the relevance score of the result item. I hope this feature will be extremely beneficial for the community members out there. 🙂

6. Category Filter

Every mine contains data from various diverse categories. So, this feature too was a necessary requirement of a full fledged searching tool. This section is loaded dynamically based on the types of categories returned by the API. The application uses the search result metadata received from the API to generate these category checkboxes dynamically. So, we need not worry about hard-coding any of these.

So, this was all about progress so far. Almost everything in the application is mobile optimized and ready to use. Most probably, I will also be extending the scope of this project and add a REST API service for searching multiple mines. So, the project will be a full fledged Cross InterMine Search Tool in future, i.e. a package of, a client driven search interface & a back-end REST API service. You can find the project repository here. Please have a look at the application here. I would love to have more feedback from the community. (For providing your feedback/suggestions, kindly email me at dwivedi.aman96@gmail.com) Thanks for reading. Happy Coding! 🙂

This is our blog series interviewing our 2018 Google Summer of Code students, who will be working remotely for InterMine for 3 months on a variety of projects. We’ve interviewed Jake Macneal, who will be working on converting natural language phrases to InterMine PathQuery.

Hi Jake! We’re really excited to have you on board as part of the team this summer. Can you introduce yourself?

Excited to be joining the team! I’m an undergraduate studying computer engineering at McGill University in Montreal, about to enter my final semester in the fall. I’m originally from Philadelphia in the US, and I’ll be hopping around North America a little bit this summer (currently in Toronto). I’ve got a passion for robotics and artificial intelligence, which led to me joining my university’s robotics team to help design and build a Mars rover. Additionally, I’ve had the opportunity to intern at NASA Johnson Space Center in Texas, where I worked on a project which uses machine learning to track sensors around the space station (hopefully it’ll be put into use soon).

Aside from those technical interests, I enjoy soccer/football (both playing and watching), classical guitar, analog synthesizers (just getting into this but they’re really fun and fascinating), and the field of space exploration. Part of me is still holding on to the hope of becoming an astronaut some day.

What interested you about GSoC with InterMine?

I searched the GSoC organizations page for projects looking for a Clojure developer, and this was unsurprisingly one of the only ones. However, a language is hardly enough motivation to become passionate about a project. I’ve never had the chance to work in bioinformatics, but I did have a beloved computer science professor (Matthieu Blanchette) whose research was in that field, and he often spoke during lectures about his research. When I read through the organization and task descriptions I immediately thought of him, and knew that this would be a cool project to join. Nothing is more rewarding to me than the thought of using software as a tool to help others do good.

Tell us about the project you’re planning to do for InterMine this summer.

InterMine uses a graph query language (PathQuery) to retrieve information from the database. My project is to implement a more user-friendly alternative, allowing non-technical users to interact with an InterMine database without the need for esoteric queries crafted by an experienced programmer or system administrator. This will take the form of a natural language to PathQuery translation tool, written as a Clojure library. In addition, I’ll be building a proof-of-concept interface allowing novice users to submit English queries which will be translated and then submitted to the query engine. This simple app will be integrated with the InterMine web app, similar to the graphical query builder.

Are there any challenges you anticipate for your project? How do you plan to overcome them?

Natural language processing is a difficult field, and from working on a compiler, I learned that the key to building a correct parser and code generator is a huge number of test cases. Fortunately, the basic principle behind testing a translation tool is simple: assemble a set of English queries, along with the intended output (in the form of a PathQuery string). However, actually assembling such a set of tests which are useful and demonstrate realistic/important queries requires interacting with actual users in the community. I hope to spend much of my initial weeks working with the community to figure out the syntax they’d like to see supported, as well as the types of queries already being written in PathQuery.